Thursday marks the start of an ambitious programme to set up immunisation clinics in 230 schools across the north. Photograph: Jeff J Mitchell/Getty Images

Staff at medical centres across Salford have been handing out warning leaflets on measles for days now. There has been a similar sense of urgency in local schools, with nurses driving home the message that teenagers who missed out on MMR vaccinations as infants should now come forward to be immunised.

In the first three weeks of April, there have been 40 reported cases of measles in the borough. Twelve have so far been confirmed but there could be others.

Across Greater Manchester, there have been 103 reported cases, with 20 of those confirmed. This, say health officials, should be seen in the context of 366 reports in the whole of 2013, with 127 cases confirmed.

"The new figures are up to date as of Tuesday afternoon," said Dr Rosemary McCann, Public Health England's local director of health protection in the north-west, as she leafed through pages of data in her office high above Eccles.

"They represent the highest number of confirmed cases in so short a period that we've had in Greater Manchester for many years. It's not at epidemic levels, but it's a very steep increase.

"Last year, there were 165 confirmed cases and this year we've already had 127. There were only 21 confirmed cases in the whole of 2011."

Most of the reported cases are of children aged between 10 and 14 – the age group who would have been eligible at the time of the MMR scare in the late 1990s and early 2000s. Local health officials always knew that a measles outbreak would be heading their way. They just didn't quite know when.

Those succumbing to the infection now came through their primary school years unscathed. In those days, says McCann, they were among small groups of non-immunised children. It was only when they moved to secondary schools that they began to mix with similarly at-risk children, and the chances of an outbreak multiplied accordingly.

The measles "bump" has been moving steadily eastward in the region – starting in Merseyside and moving into Wigan, Bolton and now Salford.

"We've already seen in Wigan and Bolton how everything was motoring along for this generation until they got to secondary school," says McCann.

"In Wigan, we're seeing transmission beyond secondary schools and into the community. In Salford it's still at the stage of being confined to secondary schools. It's contained at the moment, and we are working very hard to make sure it doesn't go any further."

About 10% of those infected with measles this year have been hospitalised. But so far McCann is unaware of any suffering serious complications.

"I think it's seven or eight years since we've had a measles death in Greater Manchester," she says. "Thankfully, we have very high take-up rates now, with Salford the highest in the country for two and five-year-olds."

Stockton-on-Tees in the north-east of England has seen a "steady increase" in measles cases since their first outbreak last September, said Professor Peter Kelly, director of public health at Stockton borough council.

The area, which is home to 550,000 people, has seen 400 confirmed or suspected cases this year, said Kelly, 20% of which have resulted in hospitalisation. "The week before last, we had 28 cases; last week there were 30." Most of those affected were 10-14 years old, he said, and some ended up seriously ill with pneumonia and other related illnesses. "There's a bit of a fallacy that measles is a mild childhood illness. I want to dispel that fallacy. It can make people very poorly indeed," he added.

Thursday marks the start of an ambitious programme to set up immunisation clinics in all 230 schools in the area. Kelly said he estimated around 8,000 children had missed out on the MMR jab entirely a decade or so ago, or had not received the full dose. In the neighbouring borough of Hartlepool, just 85% of children were immunised against measles 14 or 15 years ago, said Kelly: that figure is now more like 92 or 93%, he said.

Nurses will go to the first schools in Stockton and Hartlepool on Thursday after enough parents filled in consent forms, said Kelly.

There have been more cases in the north-east and north west – 175 and 179 respectively – than anywhere else in England this year, with the south-west and Yorkshire and Humberside both on 48.

Measles is being seen in populations considered hard-to-reach with traditionally low coverage as well as those who took a decision based on the flawed science of Andrew Wakefield not to vaccinate their child. There have been 81 cases among travellers and 41 cases among the Orthodox Jewish community. School outbreaks so far have affected less than 1% of children, but they are the major concern because of the potential spread. Small children do only limited mixing with other children. Once they get to secondary school, a virus as infectious as measles could spread rapidly and widely. There are thought to be a third of a million children aged 10-14 who had no dose of MMR and another third who had only one dose. That gives them 95% protection, but some among them will not be immune.

London and the south-east had the worst record on MMR take-up of the entire country in the early 2000s. So far this year, London has had 67 confirmed cases. Probably it is only by chance that the capital has not suffered like Swansea. In the years after the MMR scare broke in 1998, there were London boroughs where few parents were taking their children for the jab, suspicious of the reassurance that scientists and government were offering them. In Brent in 2011, take-up was still only 60% for the first jab and a very low 32% for both.

"I worry about London," said Professor David Salisbury, director of immunisation at the Department of Health. "It is a fast-moving group of people, with families coming in and moving out. Historically there is a legacy of poorer immunisation. London to its credit has done a great deal of good work to pull up immunisation coverage, but that is for the young children. People are densely packed together in London and that's just what measles like for higher levels of transmission."

In Wales, authorities are investigating whether a private clinic chain is breaking the law by offering single injection alternatives to the triple measles, mumps and rubella vaccine.

The healthcare inspectorate there is examining the role of the Children's Immunisation Centre, a Cheshire-based company that operates from a number of sites in England and has offered measles jabs in Swansea at a cost of £110 plus £50 prescription fee.

Public Health Wales, the body co-ordinating the response to the measles epidemic, has also written to the centre asking it to substantiate claims it makes on its website that single jabs are more effective than the MMR and justify its continuing links to stories about the now discredited claims of a possible association between the MMR and autism. Healthcare Inspectorate Wales says the company is not registered with them.

The Welsh government said in a separate statement: "It is disappointing that private sector providers should try and profit from a measles outbreak by asking people to pay for a vaccine; a vaccine that doesn't protect you against as many diseases as the free and safe MMR vaccination available widely on the NHS.

"The free MMR vaccination is licensed for use in the NHS. The NHS only uses licensed vaccine from quality assured providers regulated under a safety monitoring scheme run by the Medicines and Healthcare products Regulatory Agency."

No one was available from the centre to talk to the Guardian yesterday when it was contacted.The website describes its single vaccine alternatives as "comfortable and safe". Although the centre advises parents to give children vaccines against mumps as well, it admitted earlier this month it had had no mumps vaccines for three years.

• This article was amended on 26 April 2013. The original described Hartlepool as "one of Stockton-on-Tees' main towns"; in fact the two towns lie in neighbouring but separate boroughs.